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Once Mira's tower appears in enemy territory, Adventurers will begin to invade it. Players must defend the tower, starting by building some floors containing Artifacts; if the Adventures reach the top of Mira's tower and get to the Dark Crystal, the game ends. There are several types of Artifacts players can build.

At first, players start with a simple offensive Artifact, the Iron Ball, that will do light melee damage to enemies, but over time more types of Artifacts will be unlocked. Some will help defend monsters, some will do very clever—and strange—things to Adventurers attempting to invade Mira's tower. Heroes of all the tribes and Job classes from the Final Fantasy Crystal Chronicles series will storm the Darklord's lair in real time.

Monsters are summoned to battle the Adventurers trying to invade Mira's tower, since Artifacts are not enough to defend it. Players will start off with Goblins, but as the game progresses, more monsters of different ranks, such as Bombs, Cactuars, Scorpions, characters from earlier Final Fantasy games, such as Palom and Kain, and more, will be unlocked.

After the Miasma was cleared, the monsters were in a dire situation, so they holed themselves inside the massive Darklord tower where they spent their days fighting adventurers who dared trespass. In order to save the monsters, Craydall sealed himself inside the Dark Crystal. The tranquil days returned to the tower until the Darklord's only daughter was crowned in her sixteenth birthday and declared total war between monsters and people.

Mira embarks on a conquest journey aboard her Flying Tower. She arrives to a town where, despite their initial attack, the locals don't cower in fear from her sight. Tonbetty explains that thanks to the humorous-looking shape of the tower, the villagers confused it for a kind of celebration. Mira then leaves the town in order to resolve the issue.

To do so, she commands her servants, Tonberries, to find a famous hero who she could crush. In search for a hero to defeat, Mira arrives to the hideout of a caravan of burglars, in hope that by the defeating the famous Striped Brigands, she will obtain the reputation of a dreaded Darklord and lots of striped apples for pie.

However, when Mira defeats the leader of the gang, it is discovered that they are actually the Stripped Brigands, led by Bel Dat. Bel Dat, irritated by the whole ordeal, expresses that she does have a great treasure, the secret of the new Darklord being half-demon, half-Selkie and she starts to spread the secret all over the world.

After that, Mira goes on a rampage, promptly giving Tonbetty a drop kick that almost makes her head fly off. When asked to discuss the matter with his father, she quickly refuses and sent the Tonberries to find her another hero, a female adventurer ready to challenge the Darklord.

Upon defeat, the adventurer turn out to be no other than Princess Fiona of Alfitaria, who wishes Mira could serve as a bridge between people and monsters so all races could live at peace. Mira, struck by emotion, forgot to deliver the final blow, letting the princess escape.

While Mira secludes herself in her bedroom, Stiltzkin arrives at the Darklord Flying Tower, to pay a visit to his old friend, Tonbetty. Mira quickly finds out about the meeting and proceeds to punish them both, revealing Tonbetty to be a Clavat. At that moment, a legendary hero and his apprentice arrived at the steps of the Flying Tower. Postponing Tonbetty and Stiltzkin's punishment after their defeat.

After defeating Hugh Yurg, Mira is ready to deliver punishment to Tonbetty and Stiltzkin when suddenly Darklord Craydall appeared and revealed he was the one who put Tonbetty at her service. After a brief father-daughter conversation, she forgets about the punishment and embarks in the final confrontation against the king of the most prosperous kingdom. When the battle is won by Mira, she shocks the king by revealing the end of her campaign. Mira and King Leo then agree to work together to create a world where humans and monsters can live in peace. However, even when she strives for peace, she will remain the Darklord she has become.

Similar to My Life as a King, My Life as a Darklord includes downloadable content that includes extra costumes, monsters, stages, and an extra chapter after the completion of the game. Additional content is priced between 200 and 600 Wii Points.